Let's Get Wellington Moving's programme director has indicated the transport project's sequencing is still up for debate, including the timing of a second Mt Victoria tunnel.
But Transport Minister Phil Twyford insists mass rapid transit and public transport will be delivered first, ahead of roading projects, in the $6.4b plan.
The sequencing of projects was the subject of a secret letter Julie Anne Genter, Associate Transport Minister and Green MP, penned to Twyford in March this year.
The refusal to publicly release it has heightened speculation over how much influence the Greens had over the transport project, in particular, the decision to push back construction of Wellington's second Mt Victoria Tunnel.
LGWM programme director Andrew Body gave a briefing to regional councillors this week.
Body was asked whether delivering mass rapid transit before making a decision to go ahead with a second tunnel was an overriding principle of the programme.
The Cabinet paper did suggest a sequence but it was also clear business cases needed to be done, he told councillors.
"We will determine that sequencing over the next 18 months or so and if it's different than what's in the Cabinet paper, then that's what we'll have to engage with the partners and the Government about", Body said.
The investigation would consider things like early benefits, construction disruption, and utility upgrades, he said.
Ultimately LGWM partners and the Government would make decisions about funding and sequencing priorities, he said.
NZTA towed a similar line before a Transport and Infrastructure select committee last month.
Incoming chairman Brian Roche said if the business cases did not stack up, then they would not proceed and the programme would have to be "rejigged".
The Government-endorsed indicative package was announced in May this year against Treasury advice outlined in the Cabinet paper.
"Making an announcement at this stage carries significant risks, as it will raise public expectations of future investment before the costs and benefits of the package are fully understood."
Twyford is standing firm on his expectation of how LGWM will be delivered.
"Wellingtonians told us they wanted us to prioritise public transport, rapid transit and walking and cycling improvements to ease congestion and provide genuine transport choices. That's what LGWM will do.
"That's why we are going to deliver congestion-free options like rapid transit and public transport first."
National's Transport spokesman Chris Bishop said the situation showed there was a lack of clarity over what's happening.
"It begs the question if the Let's Get Wellington Moving team think one thing should happen but the Government disagrees, what happens?
"There are so many unresolved questions and issues to do with the programme, the whole thing has been a mess."
Regional council Sustainable Transport Committee deputy chairman councillor Daran Ponter said as business cases were developed politicians would undoubtedly be confronted with new information.
"We cannot close our minds to the possibilities that the business cases may come to different conclusions than we had originally intended.
"We have to be open to be challenged about some of the aspirations we might have had for the way in which things were originally going to be sequenced."